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Addressing inconsistencies in Cyperaceae and Juncaceae taxonomy: Comment on Brožová et al. (2022). Mol Phylogenet Evol 2023; 179:107665. [PMID: 36375790 DOI: 10.1016/j.ympev.2022.107665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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Brožová V, Proćków J, Záveská Drábková L. Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae. Mol Phylogenet Evol 2022; 177:107588. [PMID: 35907594 DOI: 10.1016/j.ympev.2022.107588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/06/2021] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Juncaceae is a cosmopolitan family belonging to the cyperid clade of Poales together with Cyperaceae and Thurniaceae. These families have global economic and ethnobotanical significance and are often keystone species in wetlands around the world, with a widespread cosmopolitan distribution in temperate and arctic regions in both hemispheres. Currently, Juncaceae comprises more than 474 species in eight genera: Distichia, Juncus, Luzula, Marsippospermum, Oreojuncus, Oxychloë, Patosia and Rostkovia. The phylogeny of cyperids has not been studied before in a complex view based on most sequenced species from all three families. In this study, most sequenced regions from chloroplast (rbcL, trnL, trnL-trnF) and nuclear (ITS1-5.8S-ITS2) genomes were employed from more than a thousand species of cyperids covering all infrageneric groups from their entire distributional range. We analyzed them by maximum parsimony, maximum likelihood, and Bayesian inference to revise the phylogenetic relationships in Juncaceae and Cyperaceae. Our major results include the delimitation of the most problematic paraphyletic genus Juncus, in which six new genera are recognized and proposed to recover monophyly in this group: Juncus, Verojuncus, gen. nov., Juncinella, gen. et stat. nov., Alpinojuncus, gen. nov., Australojuncus, gen. nov., Boreojuncus, gen. nov. and Agathryon, gen. et stat. nov. For these genera, a new category, Juncus supragen. et stat. nov., was established. This new classification places most groups recognized within the formal Juncus clade into natural genera that are supported by morphological characters.
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Affiliation(s)
- Viktorie Brožová
- Department of Botany, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, ul. Kożuchowska 7a, 51-631 Wrocław, Poland
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02 Praha 6, Czech Republic.
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Li YY, Chen YP, Jiang LQ, Liu ED, Luo Y, Peng H. Carexmalipoensis (Cyperaceae), a new species from southeast Yunnan, China. PHYTOKEYS 2022; 188:19-29. [PMID: 35095290 PMCID: PMC8760235 DOI: 10.3897/phytokeys.188.75401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Carexmalipoensis, a new species from southeast Yunnan, China, is here described and illustrated. It is morphologically similar to C.trichophylla in sect. Euprepes, but differs from it by its longer inflorescences and peduncles, pendulous spikes, hispidulous female glumes, densely hispidulous utricles, and longer nutlets.
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Affiliation(s)
- Yuan-Yuan Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Li-Qiong Jiang
- School of Ecology and Environmental Sciences & School of Life Sciences, Yunnan University, Kunming 650091, ChinaYunnan UniversityKunmingChina
| | - En-De Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Yuan Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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Liu L, Fan X, Tan P, Wu J, Zhang H, Han C, Chen C, Xun L, Guo W, Chang Z, Teng K. The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species. BMC PLANT BIOLOGY 2021; 21:17. [PMID: 33407132 PMCID: PMC7789143 DOI: 10.1186/s12870-020-02792-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 12/09/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms. RESULTS In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei's (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What's more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods. CONCLUSIONS The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.
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Affiliation(s)
- Lingyun Liu
- College of Grassland Science, Beijing Forestry University, Beijing, 100083 China
| | - Xifeng Fan
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Penghui Tan
- Beijing Chaoyang Foreign Language School, Beijing, 100000 China
| | - Juying Wu
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Hui Zhang
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Chao Han
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Chao Chen
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Lulu Xun
- Shaanxi Engineering Research Center for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Shaanxi, 710000 China
| | - Weier Guo
- Department of Plant Biology, University of California, Davis, Davis, CA USA
| | - Zhihui Chang
- College of Grassland Science, Beijing Forestry University, Beijing, 100083 China
| | - Ke Teng
- Beijing Research and Development Center for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
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Cui H, Zhang L, Ford B, Cheng HL, Macklin JA, Reznicek A, Starr J. Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5995854. [PMID: 33216896 PMCID: PMC7678789 DOI: 10.1093/database/baaa079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/31/2022]
Abstract
To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator-author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity. To address this problem, making scientific publications semantically clear (i.e. computable) by the authors at the time of publication is a critical step if we are to avoid postpublication curation. To help authors efficiently produce species phenotypes while producing computable data, we are experimenting with an author-driven ontology development approach and developing and evaluating a series of ontology-aware software modules that would create publishable species descriptions that are readily useable in scientific computations. The first software module prototype called Measurement Recorder has been developed to assist authors in defining continuous measurements and reported in this paper. Two usability studies of the software were conducted with 22 undergraduate students majoring in information science and 32 in biology. Results suggest that participants can use Measurement Recorder without training and they find it easy to use after limited practice. Participants also appreciate the semantic enhancement features. Measurement Recorder's character reuse features facilitate character convergence among participants by 48% and have the potential to further reduce user errors in defining characters. A set of software design issues have also been identified and then corrected. Measurement Recorder enables authors to record measurements in a semantically clear manner and enriches phenotype ontology along the way. Future work includes representing the semantic data as Resource Description Framework (RDF) knowledge graphs and characterizing the division of work between authors as domain knowledge providers and ontology engineers as knowledge formalizers in this new author-driven ontology development approach.
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Affiliation(s)
- Hong Cui
- School of Information, University of Arizona, Tucson, AZ 85705, USA
| | - Limin Zhang
- School of Information, University of Arizona, Tucson, AZ 85705, USA
| | - Bruce Ford
- Department of Biological sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hsin-Liang Cheng
- Curtis Laws Wilson Library, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - James A Macklin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Anton Reznicek
- LSA Herbarium, University of Michigan, Ann Arbor, MI 48019, USA
| | - Julian Starr
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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Léveillé-Bourret É, Chen BH, Garon-Labrecque MÈ, Ford BA, Starr JR. RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae). Mol Phylogenet Evol 2020; 145:106727. [DOI: 10.1016/j.ympev.2019.106727] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/13/2019] [Accepted: 12/29/2019] [Indexed: 12/15/2022]
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Shuryak I. Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 212:106128. [PMID: 31818732 DOI: 10.1016/j.jenvrad.2019.106128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th Street, VC-11-234/5, New York, NY, USA.
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Starr JR, Léveillé-Bourret É, Tài VA, Thị Kim Thanh NN, Ford BA. The rediscovery of the rare Vietnamese endemic Eriophorum scabriculme redefines generic limits in the Scirpo-Caricoid Clade (Cyperaceae). PeerJ 2019; 7:e7538. [PMID: 31579569 PMCID: PMC6765354 DOI: 10.7717/peerj.7538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
For those familiar with boreal bogs and wet tundra, species of Eriophorum (“the cotton grasses”) will undoubtedly represent some of the most striking and memorable taxa they have encountered. This small genus of 20 Holarctic sedge species (Cyperaceae) is remarkable because its inflorescences produce large, brilliantly white to rusty-red cottony masses when its flowers develop a perianth of highly elongated bristles after anthesis. In this study, we document the rediscovery of Eriophorum scabriculme, a narrow Vietnamese endemic known from only two collections made approximately 7 km apart near Sa Pa in Lào Cai Province over 75 years ago. Using plastid DNA sequences (matK, ndhF), embryology, and morphology, we test whether E. scabriculme is aligned within the Scirpo-Caricoid Clade (genus Khaosokia and tribes Cariceae, Dulichieae, Scirpeae, and Sumatroscirpeae) or the Ficinia Clade (Cypereae), and we determine whether its unique character combinations (≥10 elongated bristles, reduced sheathing basal leaves, 1–4 spikelets) could be evidence for a new genus or simply mark it as an unusual species within currently recognised genera. In addition, we document the discovery of seven new populations, and we extend its range westward to Lai Châu Province and southward in Lào Cai Province by more than 47 km. Our results demonstrate that Eriophorum scabriculme is best treated in the genus Trichophorum, thus re-circumscribing both genera and their limits with Scirpus s.str. In addition, we emend the description of Trichophorum scabriculme (Beetle) J.R.Starr, Lév.-Bourret & B.A. Ford, provide the first pictures and accurate illustration of the species, and assess its conservation status in Vietnam (VU, Vulnerable). Our study corroborates the fact that in such a diverse and taxonomically difficult family like the sedges, conspicuous characters like highly elongated bristles may be useful for dividing diversity, but they are no guarantee that the groups they mark are natural.
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Affiliation(s)
- Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Étienne Léveillé-Bourret
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Vũ Anh Tài
- Institute of Geography, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Bruce A Ford
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Uzma, Jiménez-Mejías P, Amir R, Hayat MQ, Hipp AL. Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ 2019; 7:e6792. [PMID: 31211007 PMCID: PMC6557248 DOI: 10.7717/peerj.6792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/15/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone-Carex L. (Cyperaceae), with ca. 2100 species worldwide-has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex. METHODS Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model. RESULTS The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan Carex flora comprises a heterogeneous sample of diversifications drawn from throughout the cosmopolitan, but mostly temperate, Carex radiation. Most radiations are relatively recent, but the widespread and diverse Himalayan Kobresia radiation arose at the early Miocene. The timing and predominance of Kobresia in high-elevation Himalayan meadows suggests that Kobresia may have excluded other Carex lineages: the success of Kobresia in the Himalayas, in other words, appears to be a consequence largely of priority, competitive exclusion and historical contingency.
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Affiliation(s)
- Uzma
- Plant Systematics and Evolution Laboratory, Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Herbarium, The Morton Arboretum, Lisle, IL, United States of America
- Pritzker DNA laboratory, The Field Museum, Chicago, IL, United States of America
| | - Pedro Jiménez-Mejías
- Department of Biology (Botany), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente, Madrid, Spain
| | - Rabia Amir
- Plant Systematics and Evolution Laboratory, Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Qasim Hayat
- Plant Systematics and Evolution Laboratory, Department of Plant Biotechnology, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Andrew L. Hipp
- Herbarium, The Morton Arboretum, Lisle, IL, United States of America
- Pritzker DNA laboratory, The Field Museum, Chicago, IL, United States of America
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